A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus)
The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals the...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Pensoft Publishers
2022-04-01
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| Series: | Metabarcoding and Metagenomics |
| Online Access: | https://mbmg.pensoft.net/article/78756/download/pdf/ |
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| author | Physilia Y. S. Chua Christian Carøe Alex Crampton-Platt Claudia S. Reyes-Avila Gareth Jones Daniel G. Streicker Kristine Bohmann |
| author_facet | Physilia Y. S. Chua Christian Carøe Alex Crampton-Platt Claudia S. Reyes-Avila Gareth Jones Daniel G. Streicker Kristine Bohmann |
| author_sort | Physilia Y. S. Chua |
| collection | DOAJ |
| description | The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data. |
| first_indexed | 2024-04-12T18:54:03Z |
| format | Article |
| id | doaj.art-796e971f4b664ff181eb218d995eb8c2 |
| institution | Directory Open Access Journal |
| issn | 2534-9708 |
| language | English |
| last_indexed | 2024-04-12T18:54:03Z |
| publishDate | 2022-04-01 |
| publisher | Pensoft Publishers |
| record_format | Article |
| series | Metabarcoding and Metagenomics |
| spelling | doaj.art-796e971f4b664ff181eb218d995eb8c22022-12-22T03:20:24ZengPensoft PublishersMetabarcoding and Metagenomics2534-97082022-04-016758710.3897/mbmg.6.7875678756A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus)Physilia Y. S. Chua0Christian Carøe1Alex Crampton-Platt2Claudia S. Reyes-Avila3Gareth Jones4Daniel G. Streicker5Kristine Bohmann6University of CopenhagenUniversity of CopenhagenNatureMetricsUniversity of CopenhagenUniversity of BristolUniversity of GlasgowUniversity of CopenhagenThe feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n = 8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and mtDNA contig assembly) to identify prey. After validating our results from detections made through metabarcoding, we accurately identified the common vampire bats’ prey in six out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138 bp to 3231 bp (median = 770 bp, Q1 = 262 bp, Q3 = 1766 bp). This opens the potential to conduct phylogenetic and phylogeographic monitoring of elusive prey species in future studies, through the analyses of blood meal metagenomic data.https://mbmg.pensoft.net/article/78756/download/pdf/ |
| spellingShingle | Physilia Y. S. Chua Christian Carøe Alex Crampton-Platt Claudia S. Reyes-Avila Gareth Jones Daniel G. Streicker Kristine Bohmann A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus) Metabarcoding and Metagenomics |
| title | A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus) |
| title_full | A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus) |
| title_fullStr | A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus) |
| title_full_unstemmed | A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus) |
| title_short | A two-step metagenomics approach for the identification and mitochondrial DNA contig assembly of vertebrate prey from the blood meals of common vampire bats (Desmodus rotundus) |
| title_sort | a two step metagenomics approach for the identification and mitochondrial dna contig assembly of vertebrate prey from the blood meals of common vampire bats desmodus rotundus |
| url | https://mbmg.pensoft.net/article/78756/download/pdf/ |
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